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- PDB-9hfu: Caprin1 peptide bound to SPOP MATH domain -

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Basic information

Entry
Database: PDB / ID: 9hfu
TitleCaprin1 peptide bound to SPOP MATH domain
Components
  • Caprin-1
  • Speckle type BTB/POZ protein
KeywordsLIGASE / Ubiquitination / Complex / Degradation
Function / homology
Function and homology information


regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / membraneless organelle assembly / intracellular membraneless organelle / generation of neurons / cell leading edge / synapse assembly ...regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / membraneless organelle assembly / intracellular membraneless organelle / generation of neurons / cell leading edge / synapse assembly / signaling adaptor activity / molecular function activator activity / P-body / molecular condensate scaffold activity / protein catabolic process / cytoplasmic stress granule / lamellipodium / negative regulation of translation / mRNA binding / synapse / dendrite / RNA binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like ...Cytoplasmic activation/proliferation-associated protein-1 C term / Cytoplasmic activation/proliferation-associated protein-1 C term / Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Speckle type BTB/POZ protein / Caprin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMakhlouf, L. / Zeqiraj, E.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome Trust222372/Z/21/Z United Kingdom
Wellcome Trust222531/Z/21/Z United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01HL159175-04 United States
CitationJournal: Biochem.J. / Year: 2025
Title: Sequence rules for a long SPOP-binding degron required for protein ubiquitylation.
Authors: Makhlouf, L. / Mishra, M. / Makhlouf, H. / Manfield, I. / Busino, L. / Zeqiraj, E.
History
DepositionNov 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle type BTB/POZ protein
B: Speckle type BTB/POZ protein
C: Caprin-1
D: Caprin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2285
Polymers36,2054
Non-polymers231
Water4,450247
1
A: Speckle type BTB/POZ protein
D: Caprin-1


Theoretical massNumber of molelcules
Total (without water)18,1032
Polymers18,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-7 kcal/mol
Surface area8340 Å2
MethodPISA
2
B: Speckle type BTB/POZ protein
C: Caprin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1263
Polymers18,1032
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-16 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.808, 60.882, 57.117
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Speckle type BTB/POZ protein


Mass: 16309.796 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: D6RDG8
#2: Protein/peptide Caprin-1 / Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / ...Cell cycle-associated protein 1 / Cytoplasmic activation- and proliferation-associated protein 1 / GPI-anchored membrane protein 1 / GPI-anchored protein p137 / GPI-p137 / p137GPI / Membrane component chromosome 11 surface marker 1 / RNA granule protein 105


Mass: 1792.894 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14444
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Dec 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.7→41.67 Å / Num. obs: 29981 / % possible obs: 99.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.71 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.9
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 2918 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.66 Å / SU ML: 0.1403 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.9328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2039 1523 5.08 %
Rwork0.1624 28444 -
obs0.1646 29967 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 1 247 2702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052526
X-RAY DIFFRACTIONf_angle_d1.02733406
X-RAY DIFFRACTIONf_chiral_restr0.062376
X-RAY DIFFRACTIONf_plane_restr0.0086428
X-RAY DIFFRACTIONf_dihedral_angle_d5.9568339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.25361030.19812577X-RAY DIFFRACTION98.57
1.75-1.820.24471570.19132590X-RAY DIFFRACTION99.93
1.82-1.890.23551190.17672606X-RAY DIFFRACTION99.85
1.89-1.980.20061390.16612556X-RAY DIFFRACTION99.67
1.98-2.080.20961140.15042585X-RAY DIFFRACTION99.93
2.08-2.210.23361130.15552615X-RAY DIFFRACTION99.6
2.21-2.380.1961630.16062558X-RAY DIFFRACTION99.67
2.38-2.620.20811480.16492588X-RAY DIFFRACTION99.82
2.62-30.22441710.16862571X-RAY DIFFRACTION99.71
3-3.780.18021570.14292573X-RAY DIFFRACTION99.38
3.78-41.660.17831390.16242625X-RAY DIFFRACTION98.33
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.482684372370.5165421379720.6119379879911.010434492090.2961294515561.28809675481-0.172698943654-0.4248347512270.2517402842660.07741734364630.07461996086680.2549543350280.00914471196146-0.2521098301930.09490575371990.0564933130756-0.01533260978740.01241959083340.1275159085810.01492221260620.1698230069323.31240526537.471341557448.74691586653
23.72970492234-0.2382786827521.746844048522.865077670532.062259191262.80762902093-0.1679875556630.3797756734310.128324243108-0.2079389225930.0505675561542-0.1930239961810.0378057686056-0.1218769860510.07411241644760.0784287943018-0.002485217816470.01437255649430.2309344407220.01096384159890.19223088735926.886800808711.0497813015-0.322672913248
32.686821469080.5921962973580.180787571172.916724511520.1559631708312.45264456820.126292163012-0.322385613501-0.0780550443590.175386514472-0.1114514459870.1246712392370.2251267253140.005863563086880.02674707293610.0718425179877-0.0137132619379-0.01970532999090.055610086290.0133787987470.08167762509859.710639611121.477894608474.01110311168
42.72323073114-0.885602337698-0.9451309676713.818189696290.003954237587065.416635691980.1568923316140.285206331722-0.281215749371-0.3711164285740.121381082421-0.177761531703-0.2663617106880.49192110798-0.03217158836580.111768128187-0.03378041574650.03146661355310.142831140770.007788031286040.071560051025817.970442061215.1076404639-10.377125292
52.308557361411.67292232037-0.3528338857953.30223667079-0.9453781062111.45964961676-0.0455351577270.00875356419259-0.236132579755-0.12975316649-0.0558138507109-0.04808729080250.160528164153-0.06572976583440.07984705010580.0473820444010.00292885162235-0.004950158718560.0522024660269-0.01007225803530.1183442794034.35401193180.338462839299-1.19088441885
65.146383583212.237349928210.4886760770742.98412171935-0.3722718051591.26684407732-0.00462626189666-0.04919732801390.1958443822150.09790357799160.05087414951170.1059581803080.0987485955275-0.07715179964860.02464181226980.03773450814730.00619503093320.01039783306070.04756473604410.004817626876180.1323974826032.2861036264311.02676037242.15903349532
77.20004272121-0.4821598543972.306540748431.57986875188-0.1378133197216.45858500904-0.285117894447-0.687369931218-0.06130867611870.196379196495-0.03124683286240.753570900604-0.516574476086-0.09063323990190.296404227550.158713773039-0.0138730304556-0.006424712641450.0959731989856-0.08110214465950.22793921290711.982929439622.74024839479.79282502005
82.62295626641-0.408322178370.1782008284533.752020252740.1678660918331.17499570035-0.09886711241880.092444958214-0.0680979700464-0.00887618892361-0.09961187962130.7364680712310.0590321284881-0.1164124798750.09518812321070.0200776776077-0.016179431718-0.009035504602650.08191882764-0.007472444381940.1196463990060.2061542621687.25772667084-3.68223230376
92.532806047622.084433376051.228246320383.170798497381.086611162541.61533381398-0.1287954691750.1516577464820.0338607706436-0.1413900271170.163784678375-0.148559896442-0.2398490435450.2286224576080.00694030921520.0626730495114-0.01380019563480.01567763900550.0752911934325-0.01319155110350.084860195009315.083674114918.8422962911-2.62946617987
103.58476381951.900966551570.1368612215462.756616162810.3487698341781.330079953680.168840214527-0.201719017795-0.1809274052930.103756989288-0.148878158119-0.0254455257615-0.05889928008460.006146243056320.00903544565970.04856908579220.00084316376203-0.005824474258970.07155878728280.004922463046970.043298663792310.780354256912.8790928017.44135222448
116.94070370175-0.07629765967570.4825321193192.403720455720.273755233221.95843503173-0.04413954480080.356645480267-0.62005483349-0.1310993631140.0456912654847-0.181656921367-0.06421233706860.281103619220.02468822727890.08642074440730.005171500225210.01405254905930.0978968428666-0.01294382220720.09875034448515.25810751794.8129589168719.6732497461
127.964341299740.02028719392373.91638961985.96587296891.578315903182.338460265150.0603815425424-1.48163033281-0.1085342661861.243544535390.244908581032-0.1162949475580.3396485175130.000650711916204-0.03075093412370.0922213706017-0.067896463075-0.08090510135690.541371602937-0.05275576383350.352410285382-7.033330259938.3315375933728.1973985613
137.4722741389-3.33394581053-3.918971916565.193196328942.275677512896.818041469550.1591529821720.16499807927-0.607133832115-0.0728516036832-0.5515904665060.8186441845290.103874239198-0.4364733955830.1179606062370.0893331244978-0.016231609202-0.0119592872480.104162661502-0.01072363708680.1166266419724.679263552551.143111853926.7142872581
144.93719199516-2.54732055994-1.874145812094.220924403611.852771933063.081715376380.206975459627-0.0380189629771-0.0457665097105-0.212703909558-0.0732190199314-0.2353696297590.1747268422510.148883038060.01136188894680.09686575818270.0393958754985-0.0005877491390070.06489925875560.01270621320290.070623492083613.6824503734-1.4569469661724.422208932
150.5137542283960.8099310299060.5546807220431.209229119470.3939161731145.962494181950.58198164085-0.4911371775340.2720119877850.5411773576220.0113102828671-0.125149861111-0.13530688704-0.294001105107-0.04065997793630.250628502172-0.03892435109290.09512287824360.263538693027-0.1385139282560.1796649104032.0375421352914.366490673938.7330845309
162.54883975447-1.4551027237-0.2616605395784.19877154480.3290869330341.65303469217-0.0985143104049-0.202111487317-0.2922801815830.1684815126070.057221825327-0.02408313044660.1763362550160.2137772106580.07918907334510.09335012346280.009618186172530.00252610040640.08543456616370.01455462923410.11387125064616.1712361862-1.5804104040130.6181073833
172.51796522065-0.0360401462161-0.0556365310541.457659939540.1973319414291.79673559462-0.08727453325570.378688233580.1886258894450.18386101187-0.139934240768-0.465178343454-0.2716155725140.4022761523680.002536559853780.0293050528467-0.0197229188541-0.009708419180780.0633579513324-0.001238308555940.18341793799917.6813500558.8894820265626.3064553074
183.406313752981.548516495994.609930060813.866175633481.770790285228.07681192558-0.03829872524090.8242276114370.290063098045-0.5291521453720.17514070969-0.139418548144-0.872620099735-0.175272145279-0.104955983640.1642708666180.03236374466580.01510868817430.2614906675280.0549262215280.2391780680476.9826602272619.217672043917.2790019694
192.11319205996-0.0206245062661-0.04196544206593.19886659674-0.2032060018161.676640131010.0167217880932-0.209156789180.1507728560680.301529106392-0.0368298477676-0.378229141998-0.07499704442310.09543578853720.004947808791830.0682378657502-0.02224498316-0.0194998753260.0948810075221-0.01721317146340.078408304495115.40947200568.9897252616332.794803891
203.102610286280.662496584513.510337224346.58047828111-2.623413140918.35333401381-0.228325475852-0.8761393420380.3003739686480.716054941269-0.2037736017430.407781364709-0.462577967827-0.8262798807910.208692994470.2199855844270.1190211561490.09751411629860.2117141119760.05066699990990.442202463484-1.7088354805621.904220000826.5701834324
214.77841287185-1.14855306298-0.2956499976213.29294102383-0.3529816013322.448911238850.1665935325870.187032647039-0.15703647466-0.0793475232231-0.06799897749120.137598322291-0.0909782192833-0.16174079706-0.08666517138220.07727966842380.00251129157859-0.01998475496450.100063428364-0.002096923958660.1042544814517.5062548241410.500708470420.6653070081
223.115309604251.707644682190.4587808931661.67388695875-1.772686865586.158259002820.173914710847-0.4459483514520.2502899101070.52551404152-0.3774222956430.035941537939-0.1729618700250.1490854978390.06558277634190.107553886307-0.04365645730420.01633823022980.15601835489-0.04083147612420.080652954678712.69069385912.508447324137.0339702805
233.191321494950.55964799730.6584035108234.753404096921.76570869273.7665145252-0.02406963453310.5679477189030.354735950173-0.507515599301-0.222522879123-0.0627610150396-0.0303351746136-0.350982269680.05564575541480.08381538653890.0278921817546-0.0003491528302990.09167692755440.01280469717040.08351579969046.7612972061212.5239824802-9.05413419922
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 38 )AA26 - 381 - 13
22chain 'A' and (resid 39 through 48 )AA39 - 4814 - 23
33chain 'A' and (resid 49 through 72 )AA49 - 7224 - 47
44chain 'A' and (resid 73 through 84 )AA73 - 8448 - 59
55chain 'A' and (resid 85 through 97 )AA85 - 9760 - 72
66chain 'A' and (resid 98 through 106 )AA98 - 10673 - 81
77chain 'A' and (resid 107 through 116 )AA107 - 11682 - 91
88chain 'A' and (resid 117 through 129 )AA117 - 12992 - 104
99chain 'A' and (resid 130 through 147 )AA130 - 147105 - 122
1010chain 'A' and (resid 148 through 166 )AA148 - 166123 - 141
1111chain 'B' and (resid 26 through 38 )BB26 - 381 - 13
1212chain 'B' and (resid 39 through 48 )BB39 - 4814 - 23
1313chain 'B' and (resid 49 through 58 )BB49 - 5824 - 33
1414chain 'B' and (resid 59 through 72 )BB59 - 7234 - 47
1515chain 'B' and (resid 73 through 84 )BB73 - 8448 - 59
1616chain 'B' and (resid 85 through 97 )BB85 - 9760 - 72
1717chain 'B' and (resid 98 through 106 )BB98 - 10673 - 81
1818chain 'B' and (resid 107 through 116 )BB107 - 11682 - 91
1919chain 'B' and (resid 117 through 138 )BB117 - 13892 - 113
2020chain 'B' and (resid 139 through 147 )BB139 - 147114 - 122
2121chain 'B' and (resid 148 through 165 )BB148 - 165123 - 140
2222chain 'C' and (resid 428 through 442 )CC428 - 4421 - 15
2323chain 'D' and (resid 428 through 442 )DD428 - 4421 - 15

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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